Bioinformatics

  • Essig K, Kronbeck N, Guimaraes JC, Lohs C, Schlundt A, Hoffmann A, Behrens G, Brenner S, Kowalska J, Lopez-Rodriguez C, Jemielity J, Holtmann H, Reiche K, Hackermüller J, Sattler M, Zavolan M, Heissmeyer V. Roquin targets mRNAs in a 3'-UTR-specific manner by different modes of regulation. Nat Commun. 2018 Sep 19;9(1):3810. dx.doi.org/10.1038/s41467-018-06184-3
  • Rehage N, Davydova E, Conrad C, Behrens G, Maiser A, Stehklein JE, Brenner S, Klein J, Jeridi A, Hoffmann A, Lee E, Dianzani U, Willemsen R, Feederle R, Reiche K, Hackermüller J, Leonhardt H, Sharma S, Niessing D, Heissmeyer V. Binding of NUFIP2 to Roquin promotes recognition and regulation of ICOS mRNA. Nat Commun. 2018 Jan 19;9(1):299. dx.doi.org/10.1038/s41467-017-02582-1
  • Binder S, Hösler N, Riedel D, Zipfel I, Buschmann T, Kämpf C, Reiche K, Burger R, Gramatzki M, Hackermüller J, Stadler PF, Horn F. STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer. Sci Rep. 2017 Aug 11;7(1):7976
  • Schüttler A, Reiche K, Altenburger R, Busch W. The Transcriptome of the Zebrafish Embryo After Chemical Exposure: A Meta-Analysis.Toxicol Sci. 2017 Jun 1;157(2):291-304.
  • Kirsten H, Al-Hasani H, Holdt L, Gross A, Beutner F, Krohn K, Horn K, Ahnert P, Burkhardt R, Reiche K, Hackermüller J, Löffler M, Teupser D, Thiery J, Scholz M. Dissecting the genetics of the human transcriptome identifies novel trait-related trans-eQTLs and corroborates the regulatory relevance of non-protein coding loci. Hum Mol Genet. 2015 May 27.
  • Nitsche A, Rose D, Fasold M, Reiche K, Stadler PF. Comparison of splice sites reveals that long noncoding RNAs are evolutionarily well conserved. RNA. 2015 May;21(5):801-12.
  • Arnold C, Externbrink F, Hackermüller J, Reiche K. CEMDesigner: Design of custom expression microarrays in the post-ENCODE Era. Journal of Biotechnology. 2014 Nov 10;189:154-6. DOI http://dx.doi.org/10.1016/j.jbiotec.2014.09.012
  • Hackermüller J, Reiche K, Otto C, Hösler N, Blumert C, Brocke-Heidrich K, Böhlig L, Nitsche A, Kasack K, Ahnert P, Krupp W, Engeland K, Stadler PF, Horn F. Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs. Genome Biol. 2014 Mar 4;15(3):R48.
  • Reiche K, Kasack K, Schreiber S, Lüders T, Due EU, Naume B, Riis M, Kristensen VN, Horn F, Børresen-Dale AL, Hackermüller J, Baumbusch LO. Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes. PLoS One. 2014 Sep 29;9(9):e106076.
  • Boll K, Reiche K, Kasack K, Mörbt N, Kretzschmar AK, Tomm JM, Verhaegh G, Schalken J, von Bergen M, Horn F, Hackermüller J. MiR-130a, miR-203 and miR-205 jointly repress key oncogenic pathways and are downregulated in prostatecarcinoma. Oncogene. 2013 Jan 17;32(3):277-85.
  • Otto C, Reiche K, Hackermüller J. Detection of differentially expressed segments in tiling array data. Bioinformatics. 2012 Jun 1;28(11):1471-9.
  • Tramontano A, Donath A, Bernhart SH, Reiche K, Böhmdorfer G, Stadler PF, Bachmair A. Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer. Virology. 2011 Mar 30;412(1):75-82.
  • Sharma CM, Hoffmann S, Darfeuille F, Reignier J, Findeiss S, Sittka A, Chabas S, Reiche K, Hackermüller J, Reinhardt R, Stadler PF, Vogel J. The primary transcriptome of the major human pathogen Helicobacter pylori. Nature. 2010 Mar 11;464(7286):250-5.
  • Kaczkowski B, Torarinsson E, Reiche K, Havgaard JH, Stadler PF, Gorodkin J. Structural profiles of human miRNA families from pairwise clustering. Bioinformatics. 2009 Feb 1;25(3):291-4.
  • Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J. NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences. Genomics. 2008 Jul;92(1):65-74.
  • Rose D, Jöris J, Hackermüller J, Reiche K, Li Q, Stadler PF. Duplicated RNA genes in teleost fish genomes. J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.
  • Athanasius F Bompfünewerer Consortium, Backofen R, Bernhart SH, Flamm C, Fried C, Fritzsch G, Hackermüller J, Hertel J, Hofacker IL, Missal K, Mosig A, Prohaska SJ, Rose D, Stadler PF, Tanzer A, Washietl S, Will S. RNAs everywhere: genome-wide annotation of structured RNAs. J Exp Zool B Mol Dev Evol. 2007 Jan 15;308(1):1-25.
  • ENCODE Project Consortium. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project. Nature. 2007 Jun 14;447(7146):799-816.
  • Reiche K, Stadler PF. RNAstrand: reading direction of structured RNAs in multiple sequence alignments. Algorithms Mol Biol. 2007 May 31;2:6.
  • Rose D, Hackermüller J, Washietl S, Reiche K, Hertel J, Findeiss S, Stadler PF, Prohaska SJ. Computational RNomics of drosophilids. BMC Genomics. 2007 Nov 8;8:406.
  • Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF. Structured RNAs in the ENCODE selected regions of the human genome. Genome Res. 2007 Jun;17(6):852-64.
  • Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Will S, Reiche K, Hofacker IL, Stadler PF, Backofen R. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Comput Biol. 2007 Apr 13;3(4):e65.
  • Hertel J, Lindemeyer M, Missal K, Fried C, Tanzer A, Flamm C, Hofacker IL, Stadler PF; Students of Bioinformatics Computer Labs 2004 and 2005. The expansion of the metazoan microRNA repertoire. BMC Genomics. 2006 Feb 15;7:25.
  • Missal K, Cross MA, Drasdo D. Gene network inference from incomplete expression data: transcriptional control of hematopoietic commitment. Bioinformatics. 2006 Mar 15;22(6):731-8.
  • Missal K, Zhu X, Rose D, Deng W, Skogerbø G, Chen R, Stadler PF. Prediction of structured non-coding RNAs in the genomes of the nematodes Caenorhabditis elegans and Caenorhabditis briggsae. J Exp Zool B Mol Dev Evol. 2006 Jul 15;306(4):379-92.
  • Missal K, Rose D, Stadler PF. Non-coding RNAs in Ciona intestinalis. Bioinformatics. 2005 Sep 1;21.
  • Bompfünewerer AF, Flamm C, Fried C, Fritzsch G, Hofacker IL, Lehmann J, Missal K, Mosig A, Müller B, Prohaska SJ, Stadler BM, Stadler PF, Tanzer A, Washietl S, Witwer C. Evolutionary patterns of non-coding RNAs. Theory Biosci. 2005 Apr;123(4):301-69.